Late to this, but I'll chime in since it worked well IMTU.
In my ATU, I adapted the plotline of Frederik Pohl's Gateway series. So, Grandfather invented jumpspace (IMTU, it was a lightspeed phenomenon, so jumpspace only covered a sphere about 200,000 light years in radius, but was expanding at a steady rate). However, at the beginning of the Universe, an even older sentient species evolved, but it was energy beings; they found the physical universe to be painful, but by the time they had discerned that the current universe would be unpleasant to live in, it was too late -- the universal constants had fallen out in such a way as to lead to a matter-heavy universe. So they cooked up a plot to increase the amount of matter in the universe to cause a Big Crunch in the future, and when the next universe started, they would be in a position to artificially alter the constants so that the next universe would be energy-based, and more to their liking. They hide out "inside"
kugelblitzes scattered throughout the universe, usually in the center of galaxies (since the high energy density of the kugelblitz usually causes an accretion disk of matter to form around it).
For the most part, the Primordials (the energy beings) bide their time in their shelters. However, they are, of course, interested in making sure no other civilization develops that can alter their plans. As a result, they have constructed Assassins, humongous objects of matter and energy and nightmarishly-advanced "technology" that can destroy whole solar systems, or (over time) arms of the galaxy. The Assassins are generally only dispatched if a threat arises, since they want as much matter and energy in the universe as possible to cause the Big Crunch, and Assassins can actually "destroy" matter and energy (actually send them to another universe, but the effect is the same). Grandfather eventually discovered the existence of the Primordials and Assassins, realized they would take an interest in the Droyne due to the expanding wave of jumpspace, and that was the cause of the Ancients going into hiding in pocket universes. Basically, you can't fight a foe who has, not thousands or hundreds of thousands, but
billions of years of a head start.
So, the Assassins leaving the core of the galaxy is a big deal, and they destroy all civilizations they come across. They started out 100,000 years ago, but were delayed destroying various civilizations and are only now getting near the region of the Third Imperium. The Empress Wave was only one of the several alarms sent out by other civilizations the Assassins have destroyed "recently". IMTU, the Zhodani projection device that led to the Core Expeditions was alerting them to the Assassins, but the Zho policy of always making the projections come to pass means they're going to be the first sophonts from this part of space to encounter the Assassins...
